Pressure in rigid body molecular dynamics

Jens Glaser; Xun Zha; Joshua A. Anderson; Sharon C. Glotzer; Alex Travesset

doi:10.1016/j.commatsci.2019.109430

Pressure in rigid body molecular dynamics

Jens Glaser, Xun Zha, Joshua A. Anderson, Sharon C. Glotzer, Alex Travesset

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

Abstract

We present a detailed derivation of the expression for the pressure in MD simulations that contain rigid bodies, where two equivalent formulations have been developed. One of these formulations was used in HOOMD-blue v1.x, but implemented incorrectly. We point out the precise reason for this implementation issue, the difference with the current and correct implementation in HOOMD-blue v2.x, and lessons learned. We perform numerical validation tests using dumbbell models, a mixture of cubic and spherical particles, and the SPC/E water model.

Original language	English
Article number	109430
Journal	Computational Materials Science
Volume	173
DOIs	https://doi.org/10.1016/j.commatsci.2019.109430
State	Published - Feb 15 2020
Externally published	Yes

Funding

This material is based upon work supported by the U.S. Army Research Laboratory and the U. S. Army Research Office under contract/Grant No. W911NF-18-1-0167 (J.G. S.C.G.). The work of XZ and AT is supported by NSF, DMR-CMMT 1606336 and used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundationgrant number ACI-1548562. Our (X.Z. and A.T.) project within XSEDE is supported by grant TG-MCB140071. This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725; INCITE Project MAT110: Nucleation and growth of colloidal crystals, and an Early Science Project on the Summit supercomputer (to S.C.G.). This research used the signac and signac-flow data and workflow management tools [33]. This material is based upon work supported by the U.S. Army Research Laboratory and the U. S. Army Research Office under contract/Grant No. W911NF-18-1-0167 (J.G., S.C.G.). The work of XZ and AT is supported by NSF, DMR-CMMT 1606336 and used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundationgrant number ACI-1548562 .. Our (X.Z. and A.T.) project within XSEDE is supported by grant TG-MCB140071 . This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC05-00OR22725; INCITE Project MAT110: Nucleation and growth of colloidal crystals, and an Early Science Project on the Summit supercomputer (to S.C.G.). This research used the signac and signac-flow data and workflow management tools [33] .

Funders	Funder number
DOE Office of Science
DOE Office of Science User Facility supported	MAT110, DE-AC05-00OR22725
Extreme Science and Engineering Discovery Environment
National Science Foundationgrant	ACI-1548562, TG-MCB140071
Oak
U. S. Army Research Office	W911NF-18-1-0167
National Science Foundation	DMR-CMMT 1606336
National Sleep Foundation
Army Research Laboratory

Keywords

Molecular dynamics
Nanoparticles
Pressure
Rigid bodies
SPC/E water model

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10.1016/j.commatsci.2019.109430

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author = "Jens Glaser and Xun Zha and Anderson, {Joshua A.} and Glotzer, {Sharon C.} and Alex Travesset",

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Pressure in rigid body molecular dynamics

Abstract

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Keywords

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